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Tutorial 2: Playing with proteins

Here, you'll see how to build, visualize, and simulate a protein structure from the PDB.



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# First, import MDT
import moldesign as mdt
from moldesign import units as u

# This sets up your notebook to draw inline plots:
%matplotlib inline
import numpy as np
from matplotlib.pylab import *

try: import seaborn
except ImportError: pass

1. Download from PDB
2. Strip water and assign forcefield
3. Set up energy model and minimize
4. Add integrator and run dynamics
5. Some simple analysis

1. Download from PDB

In this example, we'll look at 1YU8, a crystal structure of the Villin Headpiece.



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one_yu8 = mdt.read('data/1yu8.pdb')
one_yu8.draw()

By evaluating the one_yu8 variable, you can get some basic biochemical information, including metadata about missing residues in this crystal structure (hover over the amino acid sequence to get more information).



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one_yu8

2. Strip water and assign forcefield

Next, we isolate the protein and prepare it using the default Amber forcefield parameters.



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headpiece = mdt.Molecule([res for res in one_yu8.residues if res.type == 'protein'])



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ff = mdt.forcefields.DefaultAmber()
protein = ff.create_prepped_molecule(headpiece)

3. Set up energy model and minimize

Next, we'll set up a full molecular mechanics model using OpenMM, then run a minimization and visualize it.



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protein.set_energy_model(mdt.models.OpenMMPotential)



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protein.configure_methods()



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mintraj = protein.minimize()



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mintraj.draw()

4. Add integrator and run dynamics



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protein.set_integrator(mdt.integrators.OpenMMLangevin,
                       temperature=300*u.kelvin,
                       timestep=2.0*u.fs,
                       frame_interval=2.0*u.ps)



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traj = protein.run(20*u.ps)



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traj.draw()

5. Some simple analysis

As in tutorial 1, tutorial objects permit a range of timeseries-based analyses.



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# Plot kinetic energy vs. time
plot(traj.time, traj.kinetic_energy)
xlabel('time / %s' % u.default.time); ylabel('energy / %s' % u.default.energy)



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# Plot time evolution of PHE47's sidechain rotation
residue = protein.chains[0].residues['PHE47']
plot(traj.time, traj.dihedral(residue['CA'], residue['CB']).to(u.degrees))

title('sidechain rotation vs time')
xlabel('time / %s' % u.default.time); ylabel(u'angle / º')